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- PDB-3ei8: Crystal structure of K270N variant of LL-diaminopimelate aminotra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ei8 | ||||||
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Title | Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with LL-DAP: External aldimine form | ||||||
![]() | LL-diaminopimelate aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / lysine biosynthesis / Pyridoxal 5' phosphate / external aldimine / LL-diaminopimelate / Chloroplast / Pyridoxal phosphate / Transit peptide | ||||||
Function / homology | ![]() LL-diaminopimelate aminotransferase / L,L-diaminopimelate aminotransferase activity / systemic acquired resistance, salicylic acid mediated signaling pathway / transaminase activity / lysine biosynthetic process via diaminopimelate / chloroplast stroma / chloroplast / pyridoxal phosphate binding / copper ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N.G. | ||||||
![]() | ![]() Title: Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. Authors: Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.5 KB | Display | ![]() |
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PDB format | ![]() | 152.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 870.2 KB | Display | ![]() |
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Full document | ![]() | 878.5 KB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 64.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ei5C ![]() 3ei6C ![]() 3ei7C ![]() 3ei9C ![]() 3eiaC ![]() 3eibC ![]() 2z20S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47502.570 Da / Num. of mol.: 2 / Fragment: UNP residues 36 to 461 / Mutation: K270N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q93ZN9, LL-diaminopimelate aminotransferase |
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-Non-polymers , 5 types, 1026 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PL5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PL5.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PL5 / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 45% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2007 |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 137740 / Num. obs: 137740 / % possible obs: 99.8 % / Rsym value: 0.073 |
Reflection shell | Resolution: 1.6→1.66 Å / Rsym value: 0.644 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2Z20 Resolution: 1.6→39.41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.255 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.445 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.64 Å / Total num. of bins used: 20
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